The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The package scone has been added to the list. Pbase has been maintainer requested deprecated as well.
The current list of deprecated packages for Bioc 3.10 is as follows:

Maintainer requested deprecation:

Software:

SNPchip

GenomeGraphs

HTSanalyzeR

Rchemcpp

charm

Pbase

Experiment Data Package:

charmData

Unresponsive/not-maintained packages:

Software:

diggit

dSimer

flipflop

exomePeak

CNPBayes

brainImageR

plateCore

rHVDM

SEPA

viper

condcomp

PathNet

scone

Experiment Data Package:

facopy.annot

diggitdata

allenpvc

The following Annotation Packages have been user requested deprecated:

MafDb.gnomADex.r2.0.1.GRCh38

MafDb.gnomAD.r2.0.1.GRCh38

MafDb.gnomADex.r2.0.1.hs37d5

MafDb.gnomAD.r2.0.1.hs37d5

They are replaced with

MafDb.gnomADex.r2.1.GRCh38

MafDb.gnomAD.r2.1.GRCh38

MafDb.gnomADex.r2.1.hs37d5

MafDb.gnomAD.r2.1.hs37d5

We will be sending emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion.